Pre-visualization of the normalized count data before any differential analysis

Load

Libraries and functions

==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...

Data

GF_104w_F_1_2GF_104w_F_2_2GF_104w_F_3_2GF_104w_M_1_2GF_104w_M_2_2GF_52w_M_1_2GF_52w_M_2_2GF_52w_M_3_2GF_52w_M_4_2GF_8w_M_1_2SPF_104w_M_14_2SPF_8w_F_1_2SPF_8w_F_3_2SPF_8w_F_4_2SPF_8w_F_5_2GF_8w_F_1_2GF_8w_F_2_2GF_8w_F_3_2GF_8w_F_4_2GF_8w_F_5_2
0610005C13Rik 0.0000 0.00000 0.0000 1.768593 1.259244 0.8418979 4.942785 5.603216 7.231584 8.47277 5.28524 3.500355 2.112002 2.602398 0.00000 18.24998 0.00000 2.025447 5.268672 0.00000
Erg28 868.4015 749.64927 910.3535 886.064952 992.913601 508.5063502530.855142 514.375197 738.344705 603.98749 692.36648 763.077332 744.480801 908.237050 957.79030 898.54336 682.26034 612.697796 593.252445 809.27852
0610009B22Rik1021.3276 1169.19730 1180.9991 1224.750457 1558.313990 1038.9020466876.850113 1016.423320 877.914273 948.95029 1206.79653 1268.295198 1164.769254 1295.994415 1446.89758 1040.24912 1020.67017 1142.352254 959.952003 1094.00091
0610009L18Rik 28.2185 36.20465 18.2253 20.338816 38.406931 31.9921214 26.691041 22.412863 4.338950 61.73018 45.80542 42.004257 45.408049 102.794738 72.02239 48.30878 19.58642 11.139960 45.310578 24.36813
0610009O20Rik 217.5555 278.98879 266.0893 226.379868 271.996624 299.7156634349.949200 395.587025 309.511786 360.69794 178.81730 274.194454 252.384272 227.709862 184.89330 231.88216 158.86764 271.409933 304.529230 269.33199
0610010B08Rik 0.0000 0.00000 0.0000 0.000000 0.000000 0.0000000 0.000000 0.000000 0.000000 0.00000 0.00000 0.000000 0.000000 0.000000 0.00000 0.00000 0.00000 0.000000 0.000000 0.00000

Sample clustering

Gene co-expression network analysis

Build network

  1. 24421
  2. 60
  1. 10219
  2. 60
pickSoftThreshold: will use block size 4378.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 4378 of 10219
   ..working on genes 4379 through 8756 of 10219
   ..working on genes 8757 through 10219 of 10219
   Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
1      2    0.144 -0.617          0.901 644.0000  6.20e+02 1390.00
2      4    0.691 -1.460          0.964 114.0000  9.21e+01  438.00
3      6    0.783 -1.840          0.970  31.1000  1.94e+01  198.00
4      8    0.790 -2.020          0.962  11.0000  5.03e+00  106.00
5     10    0.832 -1.990          0.985   4.6100  1.49e+00   63.10
6     12    0.851 -1.960          0.988   2.1900  4.90e-01   40.10
7     14    0.876 -1.890          0.988   1.1500  1.72e-01   26.70
8     16    0.886 -1.820          0.971   0.6430  6.43e-02   18.40
9     18    0.899 -1.780          0.970   0.3830  2.50e-02   13.60
10    20    0.882 -1.770          0.946   0.2400  1.02e-02   10.40
11    22    0.917 -1.720          0.984   0.1560  4.29e-03    8.11
12    24    0.902 -1.700          0.962   0.1050  1.86e-03    6.46
13    26    0.408 -2.230          0.416   0.0724  8.32e-04    5.23
14    28    0.416 -2.190          0.427   0.0514  3.76e-04    4.28
15    30    0.931 -1.630          0.984   0.0372  1.74e-04    3.55

Parameters for network construction

  • Soft-thresholding power parameter: 16
  • Minimum module size: 25
  • Height for module merging: 0.2 (below)
  • Biweight Midcorrelation
Erg280610009B22Rik0610009L18Rik0610009O20Rik0610010F05Rik0610010K14RikMettl260610012G03Rik0610030E20Rik0610037L13RikZw10ZwintZxdaZxdbZxdcZyg11bZyxZzef1Zzz3Hikeshi
GF_104w_F_1_2868.4015 1021.328 28.21850 217.5555 411.4439 1351.757 283.0953 693.6289 899.3508449.6754 618.0761 1471.913 297.6596 130.1692 923.92821333.552 2864.633 396.8795 752.7967668.1412
GF_104w_F_2_2749.6493 1169.197 36.20465 278.9888 461.0769 1516.336 207.6443 686.8236 759.2329526.0323 797.5672 1539.763 243.8490 198.0607 981.78501340.637 3358.514 364.1762 597.3768703.8610
GF_104w_F_3_2910.3535 1180.999 18.22530 266.0893 288.8709 1852.601 222.3486 868.4353 540.3800444.6972 731.7456 1375.099 153.0925 171.3178 922.19991181.910 3058.205 209.5909 644.2642770.9300
GF_104w_M_1_2886.0650 1224.750 20.33882 226.3799 278.5534 1551.056 190.1237 823.2799 525.2720607.5116 466.9085 1752.675 172.4378 344.8756 683.56111295.494 2789.955 261.7517 944.4285687.9826
GF_104w_M_2_2992.9136 1558.314 38.40693 271.9966 304.1073 1911.532 243.0340 778.8422 707.6949586.8075 878.3224 1957.494 147.9611 249.3302 1003.61721205.726 2819.446 200.8494 785.1384583.6594
GF_52w_M_1_2508.5064 1038.902 31.99212 299.7157 392.3244 1173.606 182.6919 589.3286 1047.3210621.3207 768.6528 1397.551 287.9291 275.3006 924.40391674.535 2206.614 749.2892 1163.5029493.3522
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ....pre-clustering genes to determine blocks..
   Projective K-means:
   ..k-means clustering..
   ..merging smaller clusters...
Block sizes:
gBlocks
   1    2    3 
4997 4015 1207 
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
 ..Working on block 2 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
 ..Working on block 3 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 3 into file norm_genes_TOM-block.3.RData
 ....clustering..
 ....detecting modules..
 No modules detected in block 3
  ..reassigning 1 genes from module 1 to modules with higher KME.
  ..reassigning 1 genes from module 9 to modules with higher KME.
  ..reassigning 3 genes from module 10 to modules with higher KME.
  ..reassigning 3 genes from module 11 to modules with higher KME.
  ..reassigning 1 genes from module 14 to modules with higher KME.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.2
       Calculating new MEs...
   0    1    2    3    4    5    6    7    8    9   10   11 
8786  446  260  191   95   93   86   62   56   53   49   42 
11
  • 11 modules with between 42 and 446 genes
  • 8786 genes not assigned to a module
1433
1433

Network visualization

TOM calculation: adjacency..
..will use 4 parallel threads.
 Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
0610030E20Rik1600020E01RikZfp9741700094D03RikLrmda1810026B05RikNdufaf82010107E04Rik2210016L21Rik2310033P09RikZmpste24Zmym6Znhit2Znrd1Znrf1Znrf2Zrsr2Zscan26Zswim8Zzef1
0610030E20Rik11000100000000000100
1600020E01Rik11010100000100100110
Zfp97400100000000010000000
1700094D03Rik01010100000100000100
Lrmda00001000000000000000
1810026B05Rik11010100000100100110

Module analysis

446
[1] 1
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
11757 GO:0044446            3.822525e-17                        1        234
3148  GO:0006325            1.691165e-16                        1         59
11744 GO:0044428            1.407598e-15                        1        157
11740 GO:0044422            2.439226e-15                        1        235
13920 GO:0051276            1.389881e-14                        1         69
11225 GO:0043231            1.518125e-14                        1        295
      numInCat                                     term ontology
11757     6649             intracellular organelle part       CC
3148       723                   chromatin organization       BP
11744     3692                             nuclear part       CC
11740     6888                           organelle part       CC
13920     1058                  chromosome organization       BP
11225     9758 intracellular membrane-bounded organelle       CC
        category over_represented_pvalue under_represented_pvalue numDEInCat
3148  GO:0006325            1.691165e-16                        1         59
13920 GO:0051276            1.389881e-14                        1         69
4827  GO:0010467            2.738277e-14                        1        184
5745  GO:0016070            3.046657e-14                        1        164
17528 GO:0090304            4.206196e-14                        1        177
5987  GO:0016569            9.534743e-14                        1         48
      numInCat                            term ontology
3148       723          chromatin organization       BP
13920     1058         chromosome organization       BP
4827      4871                 gene expression       BP
5745      4006           RNA metabolic process       BP
17528     4471  nucleic acid metabolic process       BP
5987       520 covalent chromatin modification       BP
[1] 2
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
5178  GO:0012505            7.896233e-25                        1        124
8223  GO:0031984            7.378768e-23                        1         55
11755 GO:0044444            5.786768e-18                        1        173
8221  GO:0031982            7.228745e-18                        1        112
2833  GO:0005783            2.316476e-17                        1         67
18199 GO:0098827            1.247675e-16                        1         35
      numInCat                                 term ontology
5178      3583                  endomembrane system       CC
8223       802             organelle subcompartment       CC
11755     7712                     cytoplasmic part       CC
8221      3918                              vesicle       CC
2833      1558                endoplasmic reticulum       CC
18199      456 endoplasmic reticulum subcompartment       CC
        category over_represented_pvalue under_represented_pvalue numDEInCat
5349  GO:0015031            7.586032e-08                1.0000000         53
9629  GO:0034976            9.555774e-08                1.0000000         16
16645 GO:0071705            1.374311e-07                1.0000000         59
12003 GO:0045184            1.747714e-07                1.0000000         54
5634  GO:0015833            2.404955e-07                0.9999999         53
11032 GO:0042886            3.230345e-07                0.9999999         53
      numInCat                                     term ontology
5349      1761                        protein transport       BP
9629       217 response to endoplasmic reticulum stress       BP
16645     2100              nitrogen compound transport       BP
12003     1855    establishment of protein localization       BP
5634      1807                        peptide transport       BP
11032     1823                          amide transport       BP
[1] 3
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
11766 GO:0044455            2.712250e-58                        1         55
2801  GO:0005743            2.975123e-56                        1         64
6727  GO:0019866            5.893037e-55                        1         64
2798  GO:0005740            1.130974e-54                        1         70
18184 GO:0098800            1.580494e-53                        1         47
11225 GO:0043231            2.212897e-53                        1        167
      numInCat                                         term ontology
11766      185                  mitochondrial membrane part       CC
2801       401                 mitochondrial inner membrane       CC
6727       442                     organelle inner membrane       CC
2798       606                       mitochondrial envelope       CC
18184      111 inner mitochondrial membrane protein complex       CC
11225     9758     intracellular membrane-bounded organelle       CC
        category over_represented_pvalue under_represented_pvalue numDEInCat
8936  GO:0033108            4.372404e-27                        1         25
12412 GO:0046034            5.049564e-26                        1         30
4466  GO:0009167            3.405734e-25                        1         30
4427  GO:0009126            4.304702e-25                        1         30
4460  GO:0009161            5.329877e-25                        1         30
9517  GO:0034622            6.795534e-25                        1         47
      numInCat                                                  term ontology
8936        71      mitochondrial respiratory chain complex assembly       BP
12412      204                                 ATP metabolic process       BP
4466       230 purine ribonucleoside monophosphate metabolic process       BP
4427       231     purine nucleoside monophosphate metabolic process       BP
4460       233        ribonucleoside monophosphate metabolic process       BP
9517       902              cellular macromolecular complex assembly       BP
[1] 4
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] 5
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] 6
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
11625 GO:0044238            2.036962e-06                0.9999994         62
11624 GO:0044237            2.393820e-06                0.9999992         62
16644 GO:0071704            4.209145e-06                0.9999986         63
3493  GO:0006807            6.113639e-06                0.9999979         59
18998 GO:1901564            6.803428e-06                0.9999976         45
      numInCat                                      term ontology
11625     9197                 primary metabolic process       BP
11624     9220                cellular metabolic process       BP
16644     9689       organic substance metabolic process       BP
3493      8654       nitrogen compound metabolic process       BP
18998     5793 organonitrogen compound metabolic process       BP
        category over_represented_pvalue under_represented_pvalue numDEInCat
11625 GO:0044238            2.036962e-06                0.9999994         62
11624 GO:0044237            2.393820e-06                0.9999992         62
16644 GO:0071704            4.209145e-06                0.9999986         63
3493  GO:0006807            6.113639e-06                0.9999979         59
18998 GO:1901564            6.803428e-06                0.9999976         45
      numInCat                                      term ontology
11625     9197                 primary metabolic process       BP
11624     9220                cellular metabolic process       BP
16644     9689       organic substance metabolic process       BP
3493      8654       nitrogen compound metabolic process       BP
18998     5793 organonitrogen compound metabolic process       BP
[1] 7
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
995   GO:0002252                       0                        1         26
1075  GO:0002376                       0                        1         39
3585  GO:0006952                       0                        1         32
4698  GO:0009897                       0                        1         14
14118 GO:0051607                       0                        1         15
18072 GO:0098552                       0                        1         15
      numInCat                             term ontology
995        651          immune effector process       BP
1075      2168            immune system process       BP
3585      1320                 defense response       BP
4698       309 external side of plasma membrane       CC
14118      202        defense response to virus       BP
18072      499                 side of membrane       CC
        category over_represented_pvalue under_represented_pvalue numDEInCat
995   GO:0002252            0.000000e+00                        1         26
1075  GO:0002376            0.000000e+00                        1         39
3585  GO:0006952            0.000000e+00                        1         32
14118 GO:0051607            0.000000e+00                        1         15
11949 GO:0045087            5.199351e-20                        1         23
14166 GO:0051707            8.569374e-20                        1         25
      numInCat                       term ontology
995        651    immune effector process       BP
1075      2168      immune system process       BP
3585      1320           defense response       BP
14118      202  defense response to virus       BP
11949      634     innate immune response       BP
14166      832 response to other organism       BP
[1] 8
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
       category over_represented_pvalue under_represented_pvalue numDEInCat
15   GO:0000028                       0                        1          7
958  GO:0002181                       0                        1         13
1665 GO:0003676                       0                        1         41
1688 GO:0003723                       0                        1         41
1693 GO:0003729                       0                        1         12
1695 GO:0003735                       0                        1         38
     numInCat                               term ontology
15         19   ribosomal small subunit assembly       BP
958        58            cytoplasmic translation       BP
1665     3418               nucleic acid binding       MF
1688     1569                        RNA binding       MF
1693      213                       mRNA binding       MF
1695      147 structural constituent of ribosome       MF
       category over_represented_pvalue under_represented_pvalue numDEInCat
15   GO:0000028                       0                        1          7
958  GO:0002181                       0                        1         13
3204 GO:0006412                       0                        1         40
3279 GO:0006518                       0                        1         40
3493 GO:0006807                       0                        1         45
3999 GO:0008152                       0                        1         45
     numInCat                                term ontology
15         19    ribosomal small subunit assembly       BP
958        58             cytoplasmic translation       BP
3204      604                         translation       BP
3279      753           peptide metabolic process       BP
3493     8654 nitrogen compound metabolic process       BP
3999    10180                   metabolic process       BP
[1] 9
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] 10
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
11221 GO:0043227            2.855916e-07                1.0000000         43
11220 GO:0043226            8.367349e-07                0.9999999         44
11223 GO:0043229            1.105497e-06                0.9999998         42
11225 GO:0043231            1.123530e-06                0.9999998         39
8221  GO:0031982            4.139869e-06                0.9999990         23
      numInCat                                     term ontology
11221    11402               membrane-bounded organelle       CC
11220    12318                                organelle       CC
11223    11275                  intracellular organelle       CC
11225     9758 intracellular membrane-bounded organelle       CC
8221      3918                                  vesicle       CC
[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] 11
Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2874 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
        category over_represented_pvalue under_represented_pvalue numDEInCat
11748 GO:0044432            7.285038e-09                        1         11
2839  GO:0005789            1.460999e-08                        1         10
18199 GO:0098827            1.939887e-08                        1         10
10678 GO:0042175            2.188852e-08                        1         10
2833  GO:0005783            2.721879e-08                        1         16
8223  GO:0031984            4.433091e-08                        1         12
      numInCat                                                          term
11748      541                                    endoplasmic reticulum part
2839       443                                endoplasmic reticulum membrane
18199      456                          endoplasmic reticulum subcompartment
10678      462 nuclear outer membrane-endoplasmic reticulum membrane network
2833      1558                                         endoplasmic reticulum
8223       802                                      organelle subcompartment
      ontology
11748       CC
2839        CC
18199       CC
10678       CC
2833        CC
8223        CC
        category over_represented_pvalue under_represented_pvalue numDEInCat
9511  GO:0034613            2.136080e-06                0.9999997         14
16102 GO:0070727            2.316004e-06                0.9999996         14
14130 GO:0051641            2.628164e-06                0.9999995         17
3966  GO:0008104            1.348501e-05                0.9999973         16
13855 GO:0051179            3.543872e-05                0.9999909         24
      numInCat                                term ontology
9511      1609       cellular protein localization       BP
16102     1620 cellular macromolecule localization       BP
14130     2452               cellular localization       BP
3966      2461                protein localization       BP
13855     5563                        localization       BP
scatterplotThree